rs11157219

Variant names:

• chr14-41313498-A-G
• rs11157219

Your query was ambiguous. Multiple possible variants found:

• chr14-41313498-A-G
• chr14-41313498-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.234 in 152,132 control chromosomes in the GnomAD database, including 4,436 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35645 AN: 152014 Hom.: 4435 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.234 AC: 35644 AN: 152132 Hom.: 4436 Cov.: 32 AF XY: 0.233 AC XY: 17363 AN XY: 74366

African (AFR) AF: 0.164 AC: 6823 AN: 41516

American (AMR) AF: 0.212 AC: 3239 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 796 AN: 3468

East Asian (EAS) AF: 0.177 AC: 920 AN: 5186

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4826

European-Finnish (FIN) AF: 0.284 AC: 3008 AN: 10580

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18427 AN: 67966

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.256 Hom.: 13756

Bravo AF: 0.225

Asia WGS AF: 0.236 AC: 820 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.83
PhyloP100		1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11157219; hg19: chr14-41782701;